'The All-Species Living Tree' Project

'The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species of Bacteria and Archaea.[1] At one stage, 23S sequences were also collected,[2] but this has since stopped.[3]

'The All-Species Living Tree' Project logo

Currently there are over 10,950 species in the aligned dataset and several more are being added either as new species are discovered or species that are not represented in the database are sequenced. Initially the latter group consisted of 7% of species.

Similar (and more recent) projects include the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which focused on whole genome sequencing of bacteria and archaea.[4][5]

Tree

The tree was created by maximum likelihood analysis without bootstrap: consequently accuracy is traded off for size and many phylum level clades are not correctly resolved (such as the Firmicutes). (Eukaryotes not present in analysis). This 16S rRNA-based phylogenetic tree is based on the ARB-SILVA release LTPs 121 (June 2015) and contains all type species with validly published names up to December 2014.[6][7]

Domain Archaea	Thaumarchaeota       Crenarchaeota (Thermoprotei)   Euryarchaeota   Methanopyrus kandleri       Methanococcales     Eurythermea   Thermococcaceae     Thermoplasmata     Neobacteria   Methanobacteriales       Archaeoglobaceae   Halomebacteria   Methanomicrobia     Halobacteriaceae
Domain Bacteria	Thermotogales       Thermodesulfobiaceae (Firmicutes)       Synergistaceae {Clostridiales Family XV Incertae Sedis} (Firmicutes)       Caldisericum exile         Thermodesulfobacteriaceae     Aquificales       Firmicutes   Thermaerobacter         Caldicellulosiruptor       Thermoanaerobacteraceae       Thermanaeromonas toyohensis       Dictyoglomus     Thermoanaerobacterales Unnamed clade I (incl. Fervidicola)               Thermoanaerobacterales Unnamed clade II         Gelria glutamica       Clostridiales Family XVIII Incertae Sedis     Sulfobacillus           Clostridia s.s. (incl. Thermolithobacter, Negativicutes & Thermoanaerobacterales Unnamed clade III)     Bacilli (incl. Erysipelotrichia & Mollicutes)                   Actinobacteria   Chloroflexi       Thermoflexus hugenholtzii     Dehalococcoidaceae         Caldilineaceae       Ardenticatena maritima     Anaerolineaceae             Ktedonobacteria       Thermomicrobia     Chloroflexi               Nitrospiraceae       Deinococci       Thermoanaerobaculum aquaticum             Caldithrix       Gemmatimonas aurantiaca     Fibrobacter       Planctobacteria Planctomycetes   Phycisphaera mikrensis     Planctomycetales         Chlamydiales     Lentisphaerae   Oligosphaera ethanolica     Lentisphaeria     Verrucomicrobia   Opitutae     Verrucomicrobiales             Sphingobacteria Chlorobi   Ignavibacteriaceae     Chlorobiaceae       Bacteroidetes         Thiobacteria   Deltaproteobacteria       Deferrisoma carnini       Desulfovibrionales       Desulfurellaceae     Epsilonproteobacteria               Acidobacteria   Holophagae       Bryobacter aggregatus     Acidobacteriaceae             Chrysiogenaceae     Deferribacteraceae         Spirochaetales       Fusobacteriales       Elusimicrobium minutum     Armatimonadetes                 Mariprofundus ferrooxydans   Rhodobacteria   Alphaproteobacteria   Chromatibacteria   Gammaproteobacteria (paraphyletic)     Betaproteobacteria

References

1. Yarza, P.; Richter, M.; Peplies, J. R.; Euzeby, J.; Amann, R.; Schleifer, K. H.; Ludwig, W.; Glöckner, F. O.; Rosselló-Móra, R. (2008). "The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains". Systematic and Applied Microbiology. 31 (4): 241–250. doi:10.1016/j.syapm.2008.07.001. hdl:10261/103580. PMID 18692976.
2. Yarza, Pablo; Ludwig, Wolfgang; Euzéby, Jean; Amann, Rudolf; Schleifer, Karl-Heinz; Glöckner, Frank Oliver; Rosselló-Móra, Ramon (2010). "Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses". Systematic and Applied Microbiology. 33 (6): 291–299. doi:10.1016/j.syapm.2010.08.001. PMID 20817437.
3. Munoz, R. L.; Yarza, P.; Ludwig, W.; Euzéby, J.; Amann, R.; Schleifer, K. H.; Oliver Glöckner, F.; Rosselló-Móra, R. (2011). "Release LTPs104 of the All-Species Living Tree". Systematic and Applied Microbiology. 34 (3): 169–170. doi:10.1016/j.syapm.2011.03.001. PMID 21497273.
4. Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos; Pukall, Rüdiger; Dalin, Eileen; Ivanova, Natalia N.; Kunin, Victor; Goodwin, Lynne; Wu, Martin; Tindall, Brian J.; Hooper, Sean D. (December 2009). "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea". Nature. 462 (7276): 1056–1060. Bibcode:2009Natur.462.1056W. doi:10.1038/nature08656. ISSN 0028-0836. PMC 3073058. PMID 20033048.
5. Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A.; Woyke, Tanja; Göker, Markus; Parker, Charles T.; Amann, Rudolf; Beck, Brian J.; Chain, Patrick S. G.; Chun, Jongsik; Colwell, Rita R. (5 August 2014). "Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains". PLOS Biology. 12 (8): e1001920. doi:10.1371/journal.pbio.1001920. ISSN 1545-7885. PMC 4122341. PMID 25093819.
6. ARB-SILVA release LTPs 121: overview (PDF) (Report). Archived from the original (PDF) on 23 September 2015.
7. ARB-SILVA release LTPs 121: full tree (PDF) (Report). Archived from the original (PDF) on 23 September 2015.

External links